Class: Ms::Sequest::Sqt::Spectrum

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/sequest/sqt.rb

Overview

0=first_scan 1=last_scan 2=charge 3=time_to_process 4=node 5=mh 6=total_intensity 7=lowest_sp 8=num_matched_peptides 9=matches

Constant Summary collapse

Leader = 
'S'

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.set_deltacn(spectra) ⇒ Object 



280
281
282
283
284
285
286
287
288
289
290
291
292
 
# File 'lib/ms/sequest/sqt.rb', line 280

def self.set_deltacn(spectra)
  spectra.each do |spec|
    matches = spec.matches
    if matches.size > 0

      (0...(matches.size-1)).each do |i|
        matches[i].deltacn = matches[i+1].deltacn_orig 
      end
      matches[-1].deltacn = 1.1
    end
  end
  spectra
end

.spectra_from_handle(fh, base_name, percolator_results = false) ⇒ Object

assumes the first line starts with an ‘S’



239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
 
# File 'lib/ms/sequest/sqt.rb', line 239

def self.spectra_from_handle(fh, base_name, percolator_results=false)
  peptides = []
  spectra = []
  
  while line = fh.gets
    case line[0,1]
    when Ms::Sequest::Sqt::Spectrum::Leader
      spectrum = Ms::Sequest::Sqt::Spectrum.new.from_line( line )
      spectra << spectrum
      matches = []
      spectrum.matches = matches
    when Ms::Sequest::Sqt::Match::Leader
      match_klass = if percolator_results
                      Ms::Sequest::Sqt::Match::Percolator
                    else
                      Ms::Sequest::Sqt::Match
                    end
      match = match_klass.new.from_line( line )
      #match[10,3] = spectrum[0,3]
      # structs cannot set multiple values at a time :(
      match[10] = spectrum[0]
      match[11] = spectrum[1]
      match[12] = spectrum[2]
      match[15] = base_name
      matches << match
      peptides << match
      loci = []
      match.loci = loci
      matches << match
    when Ms::Sequest::Sqt::Locus::Leader
      line.chomp!
      key = line.split(Ms::Sequest::Sqt::Delimiter)[1]
      locus = Ms::Sequest::Sqt::Locus.from_line( line )
      loci << locus
    end
  end
  # set the deltacn:
  set_deltacn(spectra)
  [spectra, peptides]
end

Instance Method Details

#from_line(line) ⇒ Object

returns an array -> [the next spectra line (or nil if eof), spectrum]



296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
 
# File 'lib/ms/sequest/sqt.rb', line 296

def from_line(line)
  line.chomp!
  ar = line.split(Ms::Sequest::Sqt::Delimiter)
  self[0] = ar[1].to_i
  self[1] = ar[2].to_i
  self[2] = ar[3].to_i
  self[3] = ar[4].to_f
  self[4] = ar[5]
  self[5] = ar[6].to_f
  self[6] = ar[7].to_f
  self[7] = ar[8].to_f
  self[8] = ar[9].to_i
  self[9] = []
  self
end